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<div class="title">CUDA POA package</div>  </div>
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<p>Base docs for the cudapoa package (tbd)  
<a href="#details">More...</a></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structclaragenomics_1_1cudapoa_1_1Entry.html">claragenomics::cudapoa::Entry</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">A structure to represent a sequence entry.  <a href="structclaragenomics_1_1cudapoa_1_1Entry.html#details">More...</a><br /></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></td></tr>
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typedef std::vector&lt; <a class="el" href="structclaragenomics_1_1cudapoa_1_1Entry.html">Entry</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">claragenomics::cudapoa::Group</a></td></tr>
<tr class="memdesc:ga6b301a3a6ac7edccc403ec75e7497d32"><td class="mdescLeft">&#160;</td><td class="mdescRight">A type defining the set and order of <a class="el" href="structclaragenomics_1_1cudapoa_1_1Entry.html" title="A structure to represent a sequence entry.">Entry</a>'s in which a POA is processed. <br /></td></tr>
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Enumerations</h2></td></tr>
<tr class="memitem:ga8ece5291074f6e07073b797d34ec24d0"><td class="memItemLeft" align="right" valign="top"><a id="ga8ece5291074f6e07073b797d34ec24d0"></a>enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">claragenomics::cudapoa::StatusType</a> { <br />
&#160;&#160;<b>success</b> = 0, 
<b>exceeded_maximum_poas</b>, 
<b>exceeded_maximum_sequence_size</b>, 
<b>exceeded_maximum_sequences_per_poa</b>, 
<br />
&#160;&#160;<b>exceeded_batch_size</b>, 
<b>node_count_exceeded_maximum_graph_size</b>, 
<b>edge_count_exceeded_maximum_graph_size</b>, 
<b>seq_len_exceeded_maximum_nodes_per_window</b>, 
<br />
&#160;&#160;<b>loop_count_exceeded_upper_bound</b>, 
<b>output_type_unavailable</b>, 
<b>generic_error</b>
<br />
 }</td></tr>
<tr class="memdesc:ga8ece5291074f6e07073b797d34ec24d0"><td class="mdescLeft">&#160;</td><td class="mdescRight">CUDA POA error type. <br /></td></tr>
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<tr class="memitem:ga303d3df3e0053351dc95efab320bd037"><td class="memItemLeft" align="right" valign="top"><a id="ga303d3df3e0053351dc95efab320bd037"></a>enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudapoa.html#ga303d3df3e0053351dc95efab320bd037">claragenomics::cudapoa::OutputType</a> { <b>consensus</b> = 0x1, 
<b>msa</b> = 0x1 &lt;&lt; 1
 }</td></tr>
<tr class="memdesc:ga303d3df3e0053351dc95efab320bd037"><td class="mdescLeft">&#160;</td><td class="mdescRight">OutputType - Enum for encoding type of output. <br /></td></tr>
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Functions</h2></td></tr>
<tr class="memitem:ga81951b681c27354e2dbe7933a9f168f3"><td class="memItemLeft" align="right" valign="top">std::unique_ptr&lt; <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudapoa.html#ga81951b681c27354e2dbe7933a9f168f3">claragenomics::cudapoa::create_batch</a> (int32_t max_sequences_per_poa, int32_t device_id, cudaStream_t stream, size_t max_mem, int8_t output_mask, int16_t gap_score, int16_t mismatch_score, int16_t match_score, bool cuda_banded_alignment)</td></tr>
<tr class="memdesc:ga81951b681c27354e2dbe7933a9f168f3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Creates a new CUDA <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a> object.  <a href="group__cudapoa.html#ga81951b681c27354e2dbe7933a9f168f3">More...</a><br /></td></tr>
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<tr class="memitem:ga20324a870a7cad68e1b02dcc1d5b02a1"><td class="memItemLeft" align="right" valign="top"><a id="ga20324a870a7cad68e1b02dcc1d5b02a1"></a>
<a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudapoa.html#ga20324a870a7cad68e1b02dcc1d5b02a1">claragenomics::cudapoa::Init</a> ()</td></tr>
<tr class="memdesc:ga20324a870a7cad68e1b02dcc1d5b02a1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Initialize CUDA POA context. <br /></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<p>Base docs for the cudapoa package (tbd) </p>
<h2 class="groupheader">Function Documentation</h2>
<a id="ga81951b681c27354e2dbe7933a9f168f3"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ga81951b681c27354e2dbe7933a9f168f3">&#9670;&nbsp;</a></span>create_batch()</h2>

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          <td class="memname">std::unique_ptr&lt;<a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a>&gt; claragenomics::cudapoa::create_batch </td>
          <td>(</td>
          <td class="paramtype">int32_t&#160;</td>
          <td class="paramname"><em>max_sequences_per_poa</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int32_t&#160;</td>
          <td class="paramname"><em>device_id</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">cudaStream_t&#160;</td>
          <td class="paramname"><em>stream</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>max_mem</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int8_t&#160;</td>
          <td class="paramname"><em>output_mask</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int16_t&#160;</td>
          <td class="paramname"><em>gap_score</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int16_t&#160;</td>
          <td class="paramname"><em>mismatch_score</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int16_t&#160;</td>
          <td class="paramname"><em>match_score</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>cuda_banded_alignment</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
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</div><div class="memdoc">

<p>Creates a new CUDA <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a> object. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">max_sequences_per_poa</td><td>Maximum number of sequences per POA </td></tr>
    <tr><td class="paramname">device_id</td><td>GPU device on which to run CUDA POA algorithm </td></tr>
    <tr><td class="paramname">stream</td><td>CUDA stream to use on GPU </td></tr>
    <tr><td class="paramname">max_mem</td><td>Maximum GPU memory to use for this batch. </td></tr>
    <tr><td class="paramname">output_mask</td><td>Which outputs to produce from POA (msa, consensus) </td></tr>
    <tr><td class="paramname">gap_score</td><td>Score to be assigned to a gap </td></tr>
    <tr><td class="paramname">mismatch_score</td><td>Score to be assigned to a mismatch </td></tr>
    <tr><td class="paramname">match_score</td><td>Score to be assigned for a match </td></tr>
    <tr><td class="paramname">cuda_banded_alignment</td><td>Whether to use banded alignment</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Returns a unique pointer to a new <a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a> object </dd></dl>

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